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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.21

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        aCaMEL NextFlow DSL2 pipeline for designing GTSeq assays from genotyped SNP data

        This report has been generated by the aCaMEL/gtseqdesign analysis pipeline.

        Report generated on 2025-06-09, 20:38 UTC based on data in: /Users/tyler/projects/COL/gtseq_final/work/f1/e8022337ed2027c014595188f9bd3d

        Panel validation

        Analysis carried out to explore genetic structure of populations before and after panel generation.

        Best K by cross-validation

        Cross-validation (CV) plot for ADMIXTURE analysis run on the full filtered dataset

        ADMIXTURE Assignments for Full Dataset

        Stacked barplot showing ancestry proportions for each individual before SNP panel selection.

        ADMIXTURE Assignments for Selected Panel

        Stacked barplot showing ancestry proportions for each individual after SNP panel selection.

        Regression of Assignment Probabilities

        Comparison of minimum and maximum assignment probabilities pre vs post filtering.

        Entropy of Assignment Probabilities

        Per-sample entropy in assignment probabilities before and after filtering.

        Summary of Filtering Effects on Admixture

        Metrics summarizing the effect of filtering on ADMIXTURE-based assignment.

        Showing 1/1 rows and 11/11 columns.
        Sample NameR² (Max Assignment)Slope (Max Assignment)R² (Min Assignment)Slope (Min Assignment)Spearman Correlation (Entropy)Mean Entropy (Pre)Mean Entropy (Post)Delta Entropy% Admixed (Pre)% Admixed (Post)Delta % Admixed
        summary
        0.9
        1.1
        0.2
        0.7
        1.0
        0.4
        0.5
        0.1
        0.4
        0.4
        0.1

        Dataset Composition

        Summary statistics and plots of dataset composition before panel design.

        Summary of Filtering Steps

        Sankey diagram displaying locus loss at each sampling step performed by SNPio

        filtering_results_sankey_thresholds75.0_75.0_75_75_0.0_0.0_0_0_0.5_0.5_0_0_0.2_0.2_0_0

        Per-sample Summary Statistics

        Heterozygosity and missing data percentage pre- and post- filtering

        Showing 99/99 rows and 4/4 columns.
        Sample NameMissing_PreMissing_PostHeterozygosity_PreHeterozygosity_Post
        28BACG01
        0.8
        0.0
        0.3
        0.3
        28BACG02
        0.8
        0.2
        0.2
        0.3
        28BACG03
        0.7
        0.0
        0.2
        0.3
        28BACG04
        0.8
        0.1
        0.2
        0.3
        28BATE02
        0.9
        0.6
        0.3
        0.3
        28BATE06
        0.8
        0.2
        0.3
        0.3
        28BATE16
        0.3
        0.8
        0.2
        0.3
        28BNP01
        0.7
        0.0
        0.2
        0.3
        28BNP03
        0.8
        0.1
        0.2
        0.2
        28CRDE01
        0.7
        0.0
        0.2
        0.3
        28CRLC03
        0.9
        0.2
        0.2
        0.2
        28CRLC04
        0.9
        0.5
        0.2
        0.2
        28CRLC08
        0.9
        0.6
        0.2
        0.2
        28CRLC12
        0.9
        0.7
        0.3
        0.4
        28CRLC13
        0.9
        0.7
        0.3
        0.4
        28CRLC14
        0.8
        0.1
        0.2
        0.2
        28CRLS02
        0.8
        0.1
        0.1
        0.2
        28CRLS03
        0.8
        0.1
        0.2
        0.2
        28CRLS04
        0.8
        0.1
        0.2
        0.3
        28CRLS06
        0.9
        0.7
        0.1
        0.1
        28CRLS11
        0.6
        0.0
        0.2
        0.3
        28CRLS12
        0.9
        0.7
        0.2
        0.2
        28IZCP01
        0.8
        0.0
        0.2
        0.3
        28IZCP02
        0.8
        0.1
        0.2
        0.2
        28IZCP03
        0.8
        0.1
        0.2
        0.3
        28IZCP04
        0.8
        0.1
        0.2
        0.2
        28IZCP05
        0.8
        0.1
        0.2
        0.2
        28IZCP06
        0.9
        0.7
        0.3
        0.4
        28IZCP07
        0.9
        0.6
        0.2
        0.2
        28LOSL01
        0.7
        0.0
        0.2
        0.2
        28LOSL02
        0.7
        0.0
        0.1
        0.2
        28LOSL03
        0.7
        0.0
        0.2
        0.2
        28LOSL04
        0.7
        0.1
        0.2
        0.2
        28LOSL05
        0.7
        0.0
        0.2
        0.2
        28LOSU01
        0.8
        0.1
        0.2
        0.3
        28LOSU03
        0.7
        0.0
        0.2
        0.2
        28LOSU04
        0.7
        0.0
        0.2
        0.2
        28LOSU05
        0.7
        0.0
        0.1
        0.1
        28LOSU16
        0.8
        0.1
        0.2
        0.2
        28LOSU33
        0.7
        0.1
        0.1
        0.2
        28MRFR02
        0.8
        0.1
        0.3
        0.4
        28MRFR05
        0.9
        0.2
        0.3
        0.3
        28MRFR06
        0.7
        0.0
        0.2
        0.3
        28MRFR09
        0.7
        0.0
        0.2
        0.4
        28MRFR11
        0.9
        0.3
        0.2
        0.3
        28MRRU01
        0.8
        0.1
        0.3
        0.4
        28MRRU02
        0.8
        0.1
        0.3
        0.4
        28MRRU03
        0.8
        0.1
        0.3
        0.4
        28MRRU04
        0.8
        0.1
        0.3
        0.3
        28MRRU05
        0.8
        0.0
        0.3
        0.4
        28NWPR01
        0.8
        0.2
        0.2
        0.3
        28NWPR03
        0.9
        0.2
        0.1
        0.2
        28NWPR04
        0.9
        0.2
        0.3
        0.3
        28NWPR05
        0.9
        0.2
        0.2
        0.3
        28NWPR06
        0.9
        0.3
        0.2
        0.2
        28NWPR07
        0.9
        0.6
        0.3
        0.3
        28NWPR08
        0.9
        0.3
        0.3
        0.3
        28NWPR09
        0.9
        0.4
        0.2
        0.3
        28NWPR31
        0.6
        0.0
        0.2
        0.3
        28STCC01
        0.9
        0.4
        0.3
        0.3
        28STCC02
        0.9
        0.3
        0.3
        0.3
        28STCC03
        0.9
        0.3
        0.2
        0.2
        28STCC04
        0.9
        0.3
        0.3
        0.3
        28STCC05
        0.9
        0.2
        0.3
        0.3
        28STCC10
        0.9
        0.4
        0.2
        0.3
        28STCC11
        0.8
        0.2
        0.2
        0.3
        28STCC51
        0.3
        0.0
        0.3
        0.3
        28STCC68
        0.8
        0.1
        0.2
        0.2
        28STCE01
        0.9
        0.4
        0.3
        0.3
        28STCE02
        0.9
        0.3
        0.3
        0.3
        28STCE03
        0.9
        0.6
        0.3
        0.4
        28STCE05
        0.9
        0.6
        0.4
        0.5
        28STCE07
        0.9
        0.2
        0.4
        0.5
        28STCE08
        0.9
        0.5
        0.3
        0.4
        28STCE09
        0.9
        0.6
        0.3
        0.3
        28STCE53
        0.3
        0.0
        0.3
        0.3
        28STCE59
        0.8
        0.2
        0.3
        0.4
        28STHC01
        0.6
        0.0
        0.3
        0.4
        28STHC03
        0.7
        0.0
        0.3
        0.4
        28STHC05
        0.8
        0.1
        0.3
        0.3
        28STHC09
        0.9
        0.3
        0.2
        0.3
        28STHC15
        0.6
        0.0
        0.2
        0.3
        28STHC16
        0.8
        0.2
        0.3
        0.4
        28STHC17
        0.6
        0.0
        0.3
        0.4
        28STOP01
        0.9
        0.2
        0.3
        0.4
        28STOP02
        0.8
        0.0
        0.2
        0.3
        28STOP03
        0.8
        0.1
        0.2
        0.3
        28STOP04
        0.9
        0.3
        0.3
        0.3
        28STOP05
        0.8
        0.1
        0.2
        0.3
        28STOP06
        0.8
        0.1
        0.2
        0.3
        28STOP07
        0.9
        0.4
        0.2
        0.3
        28STOP08
        0.8
        0.1
        0.2
        0.2
        28STOP09
        0.8
        0.1
        0.2
        0.2
        28STOP11
        0.7
        0.1
        0.1
        0.2
        28STOP12
        0.5
        0.0
        0.2
        0.2
        28STOP14
        0.8
        0.1
        0.2
        0.2
        28STOP15
        0.6
        0.0
        0.2
        0.2
        28STOP17
        0.8
        0.1
        0.2
        0.2
        28STOP19
        0.4
        0.0
        0.2
        0.3

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        ADMIXTUREPIPELINEAdmixPipe3.2
        Admixture1.3
        PLINK20220402
        VCFtools0.1.16
        BCFTOOLS_QUERY_PREbcftools1.21
        BESTKawknull
        CLUMPAKAdmixPipe3.2
        CLUMPAK1.1
        COMPARE_ADMIXTUREplotly6.1.2
        CVSUMAdmixPipe3.2
        FILTER_POSITIONSbcftools1.21
        INFER_POPULATIONSawknull
        INFOCALCinfocalc1.1
        perl5.32.1
        LIST_CHROMStabix1.21
        PLOT_CVplotly6.1.2
        SAMPLE_SUMMARYpandas2.2.3
        SNPIO_CONVERT_STRUCTURESNPio1.3.6
        SNPIO_FILTERSNPio1.3.6
        TABIX_BGZIPtabix1.21
        WorkflowNextflow24.4.2
        aCaMEL/gtseqdesign1.0.dev0

        aCaMEL/gtseqdesign Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.

        Methods

        Data was processed using aCaMEL/gtseqdesign v1.0dev of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.04.2 (Di Tommaso et al., 2017) with the following command:

        nextflow run ../../gtseqdesign/main.nf -profile docker,arm --input ../gtseq_trials/COL.filter.nremover.vcf --reference ../gtseq_trials/COL.loci --popmap ../gtseq_trials/COL.popmap --fully_contained --primer_length 75 --ranking_metric I_n --max_candidates 500 --min_maf 0.2 --maxk 10 --outdir results_noind -resume -c custom.config --ind_cov 0.95 --snp_cov 0.5

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        aCaMEL/gtseqdesign Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        romantic_payne
        containerEngine
        docker
        launchDir
        /Users/tyler/projects/COL/gtseq_final
        workDir
        /Users/tyler/projects/COL/gtseq_final/work
        projectDir
        /Users/tyler/projects/gtseqdesign
        userName
        tyler
        profile
        docker,arm
        configFiles
        N/A

        Input/output options

        input
        ../gtseq_trials/COL.filter.nremover.vcf
        outdir
        results_noind
        reference
        ../gtseq_trials/COL.loci
        popmap
        ../gtseq_trials/COL.popmap

        Runtime parameters

        ind_cov
        0.95
        fully_contained
        true
        min_maf
        0.2
        ranking_metric
        I_n

        Max job request options

        max_cpus
        8
        max_memory
        16.GB

        MultiQC v1.21 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.